Merge pull request #171 from bids-standard/beliy-derivate

[WIP] Function to copy derivatives

+bids/+internal/append_to_layout.m

@@ -1,4 +1,4 @@
-function subject = append_to_layout(file, subject, modality, schema)
+function [subject, p] = append_to_layout(file, subject, modality, schema)
  %
  % appends a file to the BIDS layout by parsing it according to the provided schema
  %
@@ -40,7 +40,7 @@
  p = bids.internal.parse_filename(file, entities);
 
  % do not index json files when using the schema
- if ~isempty(p) && strcmp(p.ext, '.json')
+ if isempty(p) || (~isempty(p) && strcmp(p.ext, '.json'))
  return
  end
 

+bids/+internal/ends_with.m

@@ -0,0 +1,23 @@
+function res = ends_with(str, pattern)
+ %
+ % Checks id character array 'str' ends with 'pat'
+ %
+ % USAGE res = bids.internal.endsWith(str, pat)
+ %
+ % str - character array
+ % pat - character array
+ %
+ % __________________________________________________________________________
+ %
+ % Based on spm_file.m and spm_select.m from SPM12.
+ % __________________________________________________________________________
+
+ % Copyright (C) 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+ res = false;
+ l_pat = length(pattern);
+ if l_pat > length(str)
+ return
+ end
+ res = strcmp(str(end - l_pat + 1:end), pattern);
+
+end

+bids/+internal/get_meta_list.m

@@ -0,0 +1,92 @@
+function metalist = get_meta_list(filename, pattern)
+ %
+ % Read a BIDS's file metadata according to the inheritance principle
+ %
+ % USAGE::
+ %
+ % meta = bids.internal.get_metadata(filename, pattern = '^.*%s\\.json$')
+ %
+ % :param filename: fullpath name of file following BIDS standard
+ % :type filename: string
+ % :param pattern: Regular expression matching the metadata file (default is ``'^.*%s\\.json$'``)
+ % If provided, it must at least be ``'%s'``.
+ % :type pattern: string
+ %
+ %
+ % metalist - list of paths to metafiles
+ % __________________________________________________________________________
+
+ % Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+ % Copyright (C) 2018--, BIDS-MATLAB developers
+
+ if nargin == 1
+ pattern = '^.*%s\\.json$';
+ end
+
+ pth = fileparts(filename);
+ p = bids.internal.parse_filename(filename);
+ metalist = {};
+
+ % Default assumes we are dealing with a file in the root directory
+ % like "participants.tsv"
+ % If the file has underscore separated entities ("sub-01_T1w.nii")
+ % then we look through the hierarchy for potential metadata file associated
+ % with queried file.
+ N = 1;
+ if isfield(p, 'entities')
+ N = 3;
+ % -There is a session level in the hierarchy
+ if isfield(p.entities, 'ses') && ~isempty(p.entities.ses)
+ N = N + 1;
+ end
+ end
+
+ for n = 1:N
+
+ % List the potential metadata files associated with this file suffix type
+ % Default is to assume it is a JSON file
+ metafile = bids.internal.file_utils('FPList', pth, sprintf(pattern, p.suffix));
+
+ if isempty(metafile)
+ metafile = {};
+ else
+ metafile = cellstr(metafile);
+ end
+
+ % For all those files we find which one is potentially associated with
+ % the file of interest
+ for i = 1:numel(metafile)
+
+ p2 = bids.internal.parse_filename(metafile{i});
+ entities = {};
+ if isfield(p2, 'entities')
+ entities = fieldnames(p2.entities);
+ end
+
+ % Check if this metadata file contains
+ % - the same entity-label pairs
+ % - same suffix
+ % as its data file counterpart
+ ismeta = true;
+ if ~strcmp(p.suffix, p2.suffix)
+ ismeta = false;
+ end
+ for j = 1:numel(entities)
+ if ~isfield(p.entities, entities{j}) || ...
+ ~strcmp(p.entities.(entities{j}), p2.entities.(entities{j}))
+ ismeta = false;
+ break
+ end
+ end
+
+ % append path to list
+ if ismeta
+ metalist{end + 1, 1} = metafile{i}; %#ok<AGROW>
+ end
+
+ end
+
+ % Go up to the parent folder
+ pth = fullfile(pth, '..');
+ end
+end

+bids/+internal/get_metadata.m

@@ -1,101 +1,38 @@
-function meta = get_metadata(filename, pattern)
+function meta = get_metadata(metafile)
  %
  % Read a BIDS's file metadata according to the inheritance principle
  %
  % USAGE::
  %
- % meta = bids.internal.get_metadata(filename, pattern = '^.*%s\\.json$')
+ % meta = bids.internal.get_metadata(metafile)
  %
- % :param filename: fullpath name of file following BIDS standard
- % :type filename: string
- % :param pattern: Regular expression matching the metadata file (default is ``'^.*%s\\.json$'``)
- % If provided, it must at least be ``'%s'``.
- % :type pattern: string
+ % :param metafile: list of fullpath names of metadata files.
+ % :type metafile: string or array of strings
  %
+ % :returns: - :meta: metadata structure
  %
- % meta - metadata structure
+ % .. todo
+ %
+ % add explanation on how the inheritance principle is implemented.
  % __________________________________________________________________________
 
  % Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
  % Copyright (C) 2018--, BIDS-MATLAB developers
 
- % assume most files are of the form *_suffix.json
- % add an exception for files with no suffix, like participants.tsv
- if nargin == 1
- pattern = '^.*_?%s\\.json$';
- end
-
- pth = fileparts(filename);
- p = bids.internal.parse_filename(filename);
-
  meta = struct();
+ metafile = cellstr(metafile);
 
- N = 3;
-
- % -There is a session level in the hierarchy
- if isfield(p, 'entities') && isfield(p.entities, 'ses') && ~isempty(p.entities.ses)
- N = N + 1;
- end
-
- % -Loop from the directory where the file of interest is back to the
- % top level of the BIDS hierarchy
- for n = 1:N
-
- % -List the potential metadata files associated with this file suffix type
- % Default is to assume it is a JSON file
- metafile = bids.internal.file_utils('FPList', pth, sprintf(pattern, p.suffix));
-
- if isempty(metafile)
- metafile = {};
+ for i = 1:numel(metafile)
+ if bids.internal.ends_with(metafile{i}, '.json')
+ meta = update_metadata(meta, bids.util.jsondecode(metafile{i}), metafile{i});
  else
- metafile = cellstr(metafile);
- end
-
- % -For all those files we find which one is potentially associated with
- % the file of interest
- for i = 1:numel(metafile)
-
- p2 = bids.internal.parse_filename(metafile{i});
- entities = {};
- if isfield(p2, 'entities')
- entities = fieldnames(p2.entities);
- end
-
- % Check if this metadata file contains 
- % - the same entity-label pairs 
- % - same prefix
- % as its data file counterpart
- ismeta = true;
- if ~strcmp(p.suffix, p2.suffix)
- ismeta = false;
- end
- for j = 1:numel(entities)
- if ~isfield(p.entities, entities{j}) || ...
- ~strcmp(p.entities.(entities{j}), p2.entities.(entities{j}))
- ismeta = false;
- break
- end
- end
-
- % -Read the content of the metadata file if it is a JSON file and update
- % the metadata concerning the file of interest otherwise store the filename
- if ismeta
- if strcmp(p2.ext, '.json')
- meta = update_metadata(meta, bids.util.jsondecode(metafile{i}), metafile{i});
- else
- meta.filename = metafile{i};
- end
- end
-
+ meta.filename = metafile{i};
  end
 
- % -Go up to the parent folder
- pth = fullfile(pth, '..');
-
  end
 
  if isempty(meta)
- warning('No metadata for %s', filename);
+ warning('No metadata for %s', metafile);
  end
 
 end

+bids/+internal/parse_filename.m

@@ -53,8 +53,16 @@
  end
 
  % identidy an eventual prefix to the file
- tmp = regexp(parts{1}, '(sub)', 'split');
- p.prefix = tmp{1};
+ % and amends the sub entity accordingly
+ p.prefix = '';
+ if strfind(parts{1}, 'sub-')
+ tmp = regexp(parts{1}, '(sub-)', 'split');
+ p.prefix = tmp{1};
+ if ~isempty(p.prefix)
+ p.entities.sub = p.entities.([p.prefix 'sub']);
+ p.entities = rmfield(p.entities, [p.prefix 'sub']);
+ end
+ end
 
  % -Extra fields can be added to the structure and ordered specifically.
  if nargin == 2

+bids/+internal/starts_with.m

@@ -0,0 +1,23 @@
+function res = starts_with(str, pattern)
+ %
+ % Checks id character array 'str' starts with 'pat'
+ %
+ % USAGE res = bids.internal.startsWith(str, pat)
+ %
+ % str - character array
+ % pat - character array
+ %
+ % __________________________________________________________________________
+ %
+ % Based on spm_file.m and spm_select.m from SPM12.
+ % __________________________________________________________________________
+
+ % Copyright (C) 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+ res = false;
+ l_pat = length(pattern);
+ if l_pat > length(str)
+ return
+ end
+ res = strcmp(str(1:l_pat), pattern);
+
+end